I used to really like FogBugz but the latest version got all glitzy and went AJAX on me and now while it does some cool stuff it's gotten a lot slower. My only other complaint is that it's built to be cross-platform (PHP or ASP), which is admirable but it means that the application has to live somewhere in land of feature mediocrity on both platforms — I bet FogBugz would fly on ASP.NET.
We're not using FogBugz for feature defect tracking. We're using it as a customer management tool. For example, when you email firstname.lastname@example.org you get into a FogBugz queue. While it was great about 2 years ago we're quickly out-growing this solution.
I don't really fault FogBugz for this. When we were working with a small amount of data it was perfect, maybe we've just outgrown it?
This summer we're bringing in our army of interns (email us if you're interested) and I think we're going to build a replacement for how we use FogBugz (focused on the CRM side).